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comparison bellerophon.xml @ 2:321347bd0494 draft default tip

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planemo upload for repository https://github.com/davebx/bellerophon commit a4601aa6ae17baebc453566301a387d80bd5c3d5
author iuc
date Mon, 04 Sep 2023 07:31:57 +0000
parents 25ca5d73aedf
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1:25ca5d73aedf 2:321347bd0494
1 <tool id="bellerophon" name="Filter and merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01"> 1 <tool id="bellerophon" name="Filter and merge" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="20.01">
2 <description>chimeric reads from Arima Genomics</description> 2 <description>chimeric reads from Arima Genomics</description>
3 <macros> 3 <macros>
4 <token name="@TOOL_VERSION@">1.0</token> 4 <token name="@TOOL_VERSION@">1.0</token>
5 <token name="@VERSION_SUFFIX@">0</token> 5 <token name="@VERSION_SUFFIX@">1</token>
6 </macros> 6 </macros>
7 <requirements> 7 <requirements>
8 <requirement type="package" version="@TOOL_VERSION@">bellerophon</requirement> 8 <requirement type="package" version="@TOOL_VERSION@">bellerophon</requirement>
9 <requirement type="package" version="1.12">samtools</requirement> 9 <requirement type="package" version="1.12">samtools</requirement>
10 </requirements> 10 </requirements>
26 bellerophon 26 bellerophon
27 --forward $forward_input 27 --forward $forward_input
28 --reverse $reverse_input 28 --reverse $reverse_input
29 --quality $quality 29 --quality $quality
30 --output 'merged_out.bam' 30 --output 'merged_out.bam'
31 --threads \${GALAXY_SLOTS:-1}
31 && samtools sort --no-PG -O BAM -o '$outfile' -@ \${GALAXY_SLOTS:-1} merged_out.bam 32 && samtools sort --no-PG -O BAM -o '$outfile' -@ \${GALAXY_SLOTS:-1} merged_out.bam
32 ]]> 33 ]]>
33 </command> 34 </command>
34 <inputs> 35 <inputs>
35 <param argument="--forward" type="data" format="qname_sorted.bam,sam" label="First set of reads" 36 <param argument="--forward" type="data" format="qname_sorted.bam,sam" label="First set of reads"